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ERROR Cuffmerge for differential gene and expression analysis?

I am trying to use cufflinks-2.2.1.Linux_x86_64 for differential gene and expression analysis. First I used cufflinks with following command and got output files including transcripts.gtf. However, once I use cuffmerge I am getting an error. I am not sure if I installed it properly. please advice...

cufflinks ../sorted-SRR8136652.bam -o ../SRR8136652-cuff2.out

./cuffmerge -g ../Sus_scrofa.Sscrofa11.1.100.chr.gtf -s ../Sus_scrofa.Sscrofa10.2.dna.toplevel.fa -p 8 ../assemblies.txt

ERROR:

File "/usr/bin/cuffmerge", line 95 except getopt.error, msg: ^ SyntaxError: invalid syntax

rna-seq next-gen
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written by Kumar Kumar

Not helping with this problem itself, but is there a special reason you use such old software instead of more recent and maintained alternatives such as edgeR, limma or DESeq2?

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written by ATpoint ATpoint

Thank you for letting me know. I am doing first time such type of analysis. There is no special reason. I have alignment output files .sam and .bam files from HASAT2. I also have feature count .txt file from FeatureCounts (http://subread.sourceforge.net/).

Now I am looking for differential gene and expression analysis. Please advice which pipelines should I use for this analysis.

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written by Kumar Kumar

Here is a link for a short description on what quantification options you have with RNASeq data. It all depends on your questions :-)

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written by Kristoffer Vitting-Seerup Kristoffer Vitting-Seerup

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